Chaire Modélisation Mathématique et Biodiversité

Historical patterns of diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct and many clades experience periods of dramatic diversity loss. But most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To do so, we derive an analytical expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss, using simulation. We then study the cetaceans, a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades such as the balaneopteridae, delphinidae, phocoenidae and ziphiidae mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are remarkably consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations with a few additional species arising from clades that have been in decline over the last ~10 Myrs.

Elucidating the geographical history of diversification is critical for inferring where future diversification may occur and thus could be a valuable aid in determining conservation priorities. However, it has been difficult to recognize areas with a higher likelihood of promoting diversification. In the second hour of my course I want to show how macroevolutionary and biogeographic data can help to identify areas to preserve the evolutionary process. I reconstructed centres of origin of lineages and identified areas in the Mexican tropical dry forest that have been important centres of diversification (sources) and areas where species are maintained but where diversification is less likely to occur (diversity sinks). I used the molecular phylogeny of Bursera along with information on current species distributions. Results indicate that vast areas of the forest have historically functioned as diversity sinks, generating few or no extant Bursera lineages. Only a few areas have functioned as major engines of diversification. Long-term preservation of biodiversity may be promoted by incorporation of such knowledge in decision-making.